[English] 日本語
Yorodumi
- PDB-8cir: The FERM domain of human moesin with a bound peptide identified b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cir
TitleThe FERM domain of human moesin with a bound peptide identified by phage display
Components
  • C3P
  • Moesin
KeywordsPROTEIN BINDING / PIP / FERM domain
Function / homology
Function and homology information


regulation of lymphocyte migration / T cell aggregation / regulation of organelle assembly / T cell migration / positive regulation of early endosome to late endosome transport / membrane to membrane docking / uropod / immunological synapse formation / gland morphogenesis / positive regulation of protein localization to early endosome ...regulation of lymphocyte migration / T cell aggregation / regulation of organelle assembly / T cell migration / positive regulation of early endosome to late endosome transport / membrane to membrane docking / uropod / immunological synapse formation / gland morphogenesis / positive regulation of protein localization to early endosome / cellular response to testosterone stimulus / establishment of epithelial cell apical/basal polarity / establishment of endothelial barrier / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of podosome assembly / Sensory processing of sound by inner hair cells of the cochlea / microvillus membrane / leukocyte cell-cell adhesion / regulation of cell size / leukocyte migration / pseudopodium / Recycling pathway of L1 / microvillus / T cell proliferation / cell adhesion molecule binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / filopodium / cell periphery / adherens junction / structural constituent of cytoskeleton / positive regulation of protein catabolic process / double-stranded RNA binding / Signaling by ALK fusions and activated point mutants / apical part of cell / actin binding / regulation of cell shape / basolateral plasma membrane / vesicle / cytoskeleton / blood microparticle / apical plasma membrane / focal adhesion / signaling receptor binding / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / cell surface / extracellular space / extracellular exosome / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain ...Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
BROMIDE ION / Moesin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Leisner, T.M. / Fairhead, M. / Bountra, C. / von Delft, F. / Pearce, K.H. / Brennan, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5U54AG065187-03 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Discovery of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic approach for Alzheimer's disease.
Authors: Du, Y. / Bradshaw, W.J. / Leisner, T.M. / Annor-Gyamfi, J.K. / Qian, K. / Bashore, F.M. / Sikdar, A. / Nwogbo, F.O. / Ivanov, A.A. / Frye, S.V. / Gileadi, O. / Brennan, P.E. / Levey, A.I. / ...Authors: Du, Y. / Bradshaw, W.J. / Leisner, T.M. / Annor-Gyamfi, J.K. / Qian, K. / Bashore, F.M. / Sikdar, A. / Nwogbo, F.O. / Ivanov, A.A. / Frye, S.V. / Gileadi, O. / Brennan, P.E. / Levey, A.I. / Axtman, A.D. / Pearce, K.H. / Fu, H. / Katis, V.L.
History
DepositionFeb 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 1, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.4Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Moesin
B: Moesin
C: C3P
D: C3P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,12230
Polymers85,8004
Non-polymers2,32226
Water15,133840
1
A: Moesin
C: C3P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,11416
Polymers42,9002
Non-polymers1,21414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint5 kcal/mol
Surface area20210 Å2
MethodPISA
2
B: Moesin
D: C3P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,00814
Polymers42,9002
Non-polymers1,10812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint4 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.466, 155.391, 63.607
Angle α, β, γ (deg.)90.000, 94.280, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A

NCS domain segments:

End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth seq-IDLabel seq-ID
111METMET1 - 3382 - 339
211METMET1 - 3382 - 339
322THRTHR4 - 155 - 16
422THRTHR4 - 155 - 16

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

-
Components

-
Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Moesin / Membrane-organizing extension spike protein


Mass: 41141.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSN / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P26038
#2: Protein/peptide C3P


Mass: 1758.817 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 866 molecules

#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM sodium bromide, 100 mM bis-tris-propane, 10% ethylene glycol, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→77.7 Å / Num. obs: 74812 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.997 / Net I/σ(I): 7.8
Reflection shellResolution: 1.85→1.89 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4621 / CC1/2: 0.347 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→77.696 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.813 / SU ML: 0.109 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2408 1933 2.586 %
Rwork0.1777 72826 -
all0.179 --
obs-74759 99.96 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.484 Å2
Baniso -1Baniso -2Baniso -3
1-0.484 Å20 Å2-0.396 Å2
2---0.521 Å2-0 Å2
3---0.095 Å2
Refinement stepCycle: LAST / Resolution: 1.85→77.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5913 0 89 840 6842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126208
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165842
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.6588340
X-RAY DIFFRACTIONr_angle_other_deg0.541.5713691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5375738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.928544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.652101221
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.06110318
X-RAY DIFFRACTIONr_chiral_restr0.0810.2870
X-RAY DIFFRACTIONr_chiral_restr_other0.0320.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026901
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021219
X-RAY DIFFRACTIONr_nbd_refined0.2260.21179
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.25096
X-RAY DIFFRACTIONr_nbtor_refined0.180.22842
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23203
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2617
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0650.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.220
X-RAY DIFFRACTIONr_nbd_other0.180.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.235
X-RAY DIFFRACTIONr_mcbond_it3.5553.1262872
X-RAY DIFFRACTIONr_mcbond_other3.5463.1242871
X-RAY DIFFRACTIONr_mcangle_it4.8614.6633591
X-RAY DIFFRACTIONr_mcangle_other4.864.6643592
X-RAY DIFFRACTIONr_scbond_it4.5343.6293336
X-RAY DIFFRACTIONr_scbond_other4.5333.6293337
X-RAY DIFFRACTIONr_scangle_it6.7465.1884733
X-RAY DIFFRACTIONr_scangle_other6.7455.1884734
X-RAY DIFFRACTIONr_lrange_it8.9248.2457285
X-RAY DIFFRACTIONr_lrange_other8.82442.2447024
X-RAY DIFFRACTIONr_ncsr_local_group_10.0940.0511112
X-RAY DIFFRACTIONr_ncsr_local_group_20.0870.05312
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.094290.05008
12AX-RAY DIFFRACTIONLocal ncs0.094290.05008
23AX-RAY DIFFRACTIONLocal ncs0.087280.0501
24AX-RAY DIFFRACTIONLocal ncs0.087280.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.3421490.30953720.3155410.9170.92799.63910.305
1.898-1.950.291230.27252450.27253690.9410.94899.98140.262
1.95-2.0070.2831460.24350410.24451870.9470.961000.229
2.007-2.0680.2651240.22250280.22351540.9530.96799.96120.203
2.068-2.1360.2821190.20947640.21148850.9470.97299.95910.19
2.136-2.2110.2471240.18746380.18947620.9640.9781000.168
2.211-2.2940.2391410.17144660.17346080.9640.98299.97830.153
2.294-2.3880.2731150.17243250.17444410.960.98199.97750.152
2.388-2.4940.2661200.17341080.17642280.9620.9821000.153
2.494-2.6160.191910.1539780.15140690.9770.9871000.136
2.616-2.7570.199950.15437540.15538500.9780.98699.9740.141
2.757-2.9240.2281060.1635470.16236540.9690.98599.97260.151
2.924-3.1250.231700.17933680.1834380.9670.9811000.171
3.125-3.3750.241900.18531180.18732080.9670.9821000.183
3.375-3.6970.228660.17428770.17529430.9650.9851000.175
3.697-4.1320.224610.14426170.14526780.9740.9881000.15
4.132-4.7690.177810.13622650.13823460.9820.9891000.145
4.769-5.8350.218400.1619680.16220080.980.9891000.168
5.835-8.2290.279480.18315020.18615500.9670.9831000.192
8.229-77.6960.371240.1888470.1938720.9380.97499.88530.195

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more